NM_020975.6(RET):c.539G>A (p.Arg180Gln) AND Aganglionic megacolon

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 1, 2014
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000148786.4

Allele description [Variation Report for NM_020975.6(RET):c.539G>A (p.Arg180Gln)]

NM_020975.6(RET):c.539G>A (p.Arg180Gln)

Gene:

RET:ret proto-oncogene [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q11.21

Genomic location:

Preferred name:

NM_020975.6(RET):c.539G>A (p.Arg180Gln)

HGVS:

NC_000010.11:g.43102543G>A
NG_007489.1:g.30475G>A
NM_000323.2:c.539G>A
NM_001406743.1:c.539G>A
NM_001406744.1:c.539G>A
NM_001406759.1:c.539G>A
NM_001406760.1:c.539G>A
NM_001406761.1:c.410G>A
NM_001406762.1:c.410G>A
NM_001406763.1:c.539G>A
NM_001406764.1:c.410G>A
NM_001406765.1:c.539G>A
NM_001406768.1:c.410G>A
NM_001406769.1:c.539G>A
NM_001406771.1:c.539G>A
NM_001406772.1:c.539G>A
NM_001406773.1:c.539G>A
NM_001406774.1:c.410G>A
NM_001406779.1:c.539G>A
NM_001406780.1:c.539G>A
NM_001406781.1:c.539G>A
NM_001406782.1:c.539G>A
NM_001406783.1:c.410G>A
NM_001406785.1:c.539G>A
NM_001406786.1:c.410G>A
NM_001406787.1:c.539G>A
NM_020629.2:c.539G>A
NM_020630.7:c.539G>A
NM_020975.6:c.539G>AMANE SELECT
NP_000314.1:p.Arg180Gln
NP_001393672.1:p.Arg180Gln
NP_001393673.1:p.Arg180Gln
NP_001393688.1:p.Arg180Gln
NP_001393689.1:p.Arg180Gln
NP_001393690.1:p.Arg137Gln
NP_001393691.1:p.Arg137Gln
NP_001393692.1:p.Arg180Gln
NP_001393693.1:p.Arg137Gln
NP_001393694.1:p.Arg180Gln
NP_001393697.1:p.Arg137Gln
NP_001393698.1:p.Arg180Gln
NP_001393700.1:p.Arg180Gln
NP_001393701.1:p.Arg180Gln
NP_001393702.1:p.Arg180Gln
NP_001393703.1:p.Arg137Gln
NP_001393708.1:p.Arg180Gln
NP_001393709.1:p.Arg180Gln
NP_001393710.1:p.Arg180Gln
NP_001393711.1:p.Arg180Gln
NP_001393712.1:p.Arg137Gln
NP_001393714.1:p.Arg180Gln
NP_001393715.1:p.Arg137Gln
NP_001393716.1:p.Arg180Gln
NP_065680.1:p.Arg180Gln
NP_065681.1:p.Arg180Gln
NP_065681.1:p.Arg180Gln
NP_065681.1:p.Arg180Gln
NP_066124.1:p.Arg180Gln
NP_066124.1:p.Arg180Gln
LRG_518t1:c.539G>A
LRG_518t2:c.539G>A
LRG_518:g.30475G>A
LRG_518p1:p.Arg180Gln
LRG_518p2:p.Arg180Gln
NC_000010.10:g.43597991G>A
NM_020630.4:c.539G>A
NM_020630.6:c.539G>A
NM_020975.4:c.539G>A

Protein change:

R137Q

Links:

dbSNP: rs370736139

NCBI 1000 Genomes Browser:

rs370736139

Molecular consequence:

NM_000323.2:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406743.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406744.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406759.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406760.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406761.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406762.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406763.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406764.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406765.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406768.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406769.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406771.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406772.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406773.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406774.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406779.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406780.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406781.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406782.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406783.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406785.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406786.1:c.410G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406787.1:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020629.2:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020630.7:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020975.6:c.539G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Aganglionic megacolon (HSCR)
Synonyms:: Hirschsprung's disease; Hirschsprung disease
Identifiers:: MONDO: MONDO:0018309; MeSH: D006627; MedGen: C0019569; Orphanet: 388; OMIM: PS142623; Human Phenotype Ontology: HP:0002251

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000190524	CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation	criteria provided, single submitter (Amendola et al. (Genome Res. 2015))	Uncertain significance (Jun 1, 2014)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000190524

CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation

criteria provided, single submitter

(Amendola et al. (Genome Res. 2015))

Uncertain significance
(Jun 1, 2014)

germline

research

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

Actionable exomic incidental findings in 6503 participants: challenges of variant classification.

Amendola LM, Dorschner MO, Robertson PD, Salama JS, Hart R, Shirts BH, Murray ML, Tokita MJ, Gallego CJ, Kim DS, Bennett JT, Crosslin DR, Ranchalis J, Jones KL, Rosenthal EA, Jarvik ER, Itsara A, Turner EH, Herman DS, Schleit J, Burt A, Jamal SM, et al.

Genome Res. 2015 Mar;25(3):305-15. doi: 10.1101/gr.183483.114. Epub 2015 Jan 30.

PubMed [citation]

PMID:: 25637381
PMCID:: PMC4352885

Details of each submission

From CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation, SCV000190524.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)

Description

Low GERP score may suggest that this variant may belong in a lower pathogenicity class

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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